Analysis of gene expression and histone modification between C4 and non-C4 homologous genes of PPDK and PCK in maize

Abstract

More efficient photosynthesis has allowed C4 plants to adapt to more diverse ecosystems (such as hot and arid conditions) than C3 plants. To better understand C4 photosynthesis, we investigated the expression patterns of C4 genes (C4PPDK and PCK1) and their non-C4 homologous genes (CyPPDK1, CyPPDK2, and PCK2) in the different organs of maize (Zea mays). Both C4 genes and non-C4 genes showed organ-dependent expression patterns. The mRNA levels of C4 genes were more abundant in leaf organ than in seeds at 25 days after pollination (DAP), while non-C4 genes were mainly expressed in developing seeds. Further, acetylation of histone H3 lysine 9 (H3K9ac) positively correlates with mRNA levels of C4 genes (C4PPDK and PCK1) in roots, stems, leaves, and seeds at 25 DAP, acetylation of histone H4 lysine 5 (H4K5ac) in the promoter regions of both C4 (C4PPDK and PCK1) and non-C4 genes (CyPPDK1, CyPPDK2, and PCK2) correlated well with their transcripts abundance in stems. In photosynthetic organs (stems and leaves), dimethylation of histone H3 lysine 9 (H3K9me2) negatively correlated with mRNA levels of both C4 and non-C4 genes. Taken together, our data suggest that histone modification was involved in the transcription regulation of both C4 genes and non-C4 genes, which might provide a clue of the functional evolution of C4 genes.

Histone Acetylation Modifications Affect Tissue-Dependent Expression of Poplar Homologs of C4 Photosynthetic Enzyme Genes

“…We found these nine poplar homologs of C 4 genes had tissue-dependent expression pattern. For example, PsnCA3 , PsnPPDK1-1 , and PsnPCK1 are highly expressed in photosynthetic tissue leaves ( Figure 2 ), which is consistent with the reported expression patterns of their homologous genes in C 3 herbaceous species and C 4 gramineous species (Fett and Coleman, 1994; Malone et al, 2007; Taylor et al, 2010; Langdale, 2011; Dong et al, 2016). However, not all poplar photosynthetic gene expression patterns are conserved with their homologs in other species.…”

“…Our finding that for almost all genes, the peak of H3K9ac and H4K5ac accumulation was highest in the P3 region close to the TIS ( Figures 3 , 4 ) suggests that the nucleosomes adjacent to the TIS of active genes are hypoacetylated compared to the surrounding regions. Similar observations were also made in Arabidopsis and Maize, where peaks of H3K9ac and H4K5ac accumulation were found around the ATG position, especially in photosynthesis genes (Zhou et al, 2010; Perduns et al, 2015; Dong et al, 2016). In the C 4 plant maize, PPDK and PCK gene expression is regulated by histone modifications (Dong et al, 2016).…”

“…Much of the regulation of C 4 photosynthetic enzyme expression takes place at the promoter (Sheen, 1999; Taniguchi et al, 2000; Hibberd and Covshoff, 2010), and increasing evidence indicates that histone modification plays an important role in the regulation of tissue-specific expression of CA , PPDK , PCK , PEPC , and RbcS2 in C 4 plants (Offermann et al, 2008; Heimann et al, 2013; Dong et al, 2016). Except for studies on the role of histone acetylation modifications in the regulation of the RbcA and RbcS genes during Pinus radiate needle development (Charron et al, 2009; Valledor et al, 2015), the role of histone modifications in the regulation of photosynthesis genes in C 3 plants has not been well studied.…”

“…The lower the M -value is, the more stable the gene expression (Bustin et al, 2009). We also used geNorm software to select the most stable reference genes (Dong et al, 2016). Based on geNorm analysis, ACTIN2 and EF1a were the most stable genes among the five candidate reference genes (Supplemental Figure S2B).…”

“…Current evidence suggests that increases in the level of H3K9ac and H4K5ac in the promoters of C 4 photosynthetic enzyme genes upon illumination are linked to transcriptional activation (Heimann et al, 2013). A recent study showed that C 4 -PPDK , C 4 -PCK , and their non-C 4 homologous genes have organ-specific expression patterns, and in maize the level of H3K9ac and H4K5ac modifications correlates well with the mRNA level of most PPDK and PCK genes (Dong et al, 2016). Given that genes encoding C 4 photosynthetic enzyme evolved from their C 3 counterparts, it is hypothesized that similar regulatory mechanisms may underlie the regulation of these homologous gene expressions in C 3 plants.…”